I used gencode human reference genome release 41 (https://www.gencodegenes.org/human/release_41.html) to align my fastq files. Specifically I used the first GTF file in that link to create the indexes for STAR. Now I am trying to use PICARD to get ribosome metrics but am having trouble creating the ribosome interval file.
First, do I have to use the same gtf file to get the ribosome intervals for Picard in a bed format? I tried to create the bed file of ribosome intervals with 5 columns (chr, start, stop, strand, gene id) with the basic gene annotation gtf not the first gtf file in the link ( which I used for STAR) and am getting an error of interval not within the sequence.
Second, am I doing it correctly where I am using the GTF reference genome file to get the ribosomomal sequences, then converting those sequence positions into a bed file to input as ribosome_interval.list file to get ribosome metrics?
I appreciate any help.